It all depends. Are you running on an inertial or a load (eddy current, water brake, etc. ) dyno? If you're running on an inertial dyno, the greater inertia of larger wheels and tires may leave less power available to accelerate the rollers which will drop horsepower/torque readings somewhat. On a load dyno, being more steady-state, larger wheels and tires shouldn't matter as much.
On an inertial dyno, my experience says make the run in the highest gear possible since this "tricks" the engine into thinking the rollers have more inertia and will load the engine more, helping turbo spoolup, etc. I made around 325/650 on a Dynojet 246C with 2 pulls in 5th as opposed to 347/762 with 2 pulls in 6th. On a load dyno, I'd run in 5th (direct) to minimize drivetrain losses.
Rusty